The jpredapi Tutorial¶
The jpredapi package provides functions to submit, check status, and
retrieve results from JPred: A Secondary Structure Prediction Server (JPred).
Command Line Interface¶
jpredapi command-line interface
The RESTful API allows JPred users to submit jobs from the command-line.
Usage:
jpredapi submit (--mode=<mode> --format=<format>) (--file=<filename> | --seq=<sequence>)
[--email=<name@domain.com>] [--name=<name>] [--rest=<address>] [--skipPDB] [--silent]
jpredapi status (--jobid=<id>) [--results=<path>] [--wait=<interval>] [--attempts=<max>]
[--rest=<address>] [--jpred4=<address>] [--extract] [--silent]
jpredapi get_results (--jobid=<id>) [--results=<path>] [--wait=<interval>] [--attempts=<max>]
[--rest=<address>] [--jpred4=<address>] [--extract] [--silent]
jpredapi quota (--email=<name@domain.com>) [--silent]
jpredapi check_rest_version [--rest=<address>] [--silent]
jpredapi -h | --help
jpredapi -v | --version
Options:
-h, --help Show this help message.
-v, --version Show jpredapi package version.
--silent Do not print messages.
--extract Extract results tar.gz archive.
--skipPDB PDB check.
--mode=<mode> Submission mode, possible values: single, batch, msa.
--format=<format> Submission format, possible values: raw, fasta, msf, blc.
--file=<filename> Filename of a file with the job input (sequence(s)).
--seq=<sequence> Instead of passing input file, for single-sequence submission.
--email=<name@domain.com> E-mail address where job report will be sent (optional for all but batch submissions).
--name=<name> Job name.
--jobid=<id> Job id.
--results=<path> Path to directory where to save archive with results.
--rest=<address> REST address of server [default: http://www.compbio.dundee.ac.uk/jpred4/cgi-bin/rest].
--jpred4=<address> Address of Jpred4 server [default: http://www.compbio.dundee.ac.uk/jpred4].
--wait=<interval> Wait interval before retrying to check job status in seconds [default: 60].
--attempts=<max> Maximum number of attempts to check job status [default: 10].
Print jpredapi help message¶
$ python3 -m jpredapi --help
Print jpredapi version¶
$ python3 -m jpredapi --version
Submit jobs to JPred server¶
Submit single sequence in raw format using --seq parameter:¶
python3 -m jpredapi submit --mode=single --format=raw --seq=MQVWPIEGIKKFETLSYLPP
Submit single sequence in raw format using --file parameter:¶
python3 -m jpredapi submit --mode=single --format=raw --file=tests/example_data/single_raw.example
Content of single_raw.example file:
MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC
Submit single sequence in fasta format using --file parameter:¶
python3 -m jpredapi submit --mode=single --format=fasta --file=tests/example_data/single_fasta.example
Content of single_fasta.example file:
>my test sequence
MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC
Submit multiple sequences in fasta format using --file parameter:¶
python3 -m jpredapi submit --mode=batch --format=fasta --file=tests/example_data/batch_fasta.example --email=name@domain.com
Content of batch_fasta.example file:
>my_seq1
MKFLVLLFNILCLFPILGADELVMSPIPTTDVQPKVTFDINSEVSSGPLYLNPVEMAGVK
YLQLQRQPGVQVHKVVEGDIVIWENEEMPLYTCAIVTQNEVPYMAYVELLEDPDLIFFLK
EGDQWAPIPEDQYLARLQQLRQQIHTESFFSLNLSFQHENYKYEMVSSFQHSIKMVVFTP
KNGHICKMVYDKNIRIFKALYNEYVTSVIGFFRGLKLLLLNIFVIDDRGMIGNKYFQLLD
DKYAPISVQGYVATIPKLKDFAEPYHPIILDISDIDYVNFYLGDATYHDPGFKIVPKTPQ
CITKVVDGNEVIYESSNPSVECVYKVTYYDKKNESMLRLDLNHSPPSYTSYYAKREGVWV
TSTYIDLEEKIEELQDHRSTELDVMFMSDKDLNVVPLTNGNLEYFMVTPKPHRDIIIVFD
GSEVLWYYEGLENHLVCTWIYVTEGAPRLVHLRVKDRIPQNTDIYMVKFGEYWVRISKTQ
>my_seq2
MASVKSSSSSSSSSFISLLLLILLVIVLQSQVIECQPQQSCTASLTGLNVCAPFLVPGSP
TASTECCNAVQSINHDCMCNTMRIAAQIPAQCNLPPLSCSAN
>my_seq3
MEKKSIAGLCFLFLVLFVAQEVVVQSEAKTCENLVDTYRGPCFTTGSCDDHCKNKEHLLS
GRCRDDVRCWCTRNC
Submit multiple sequence alignment files in fasta format:¶
python3 -m jpredapi submit --mode=msa --format=fasta --file=tests/example_data/msa_fasta.example --email=name@domain.com
Content of msa_fasta.example file:
>QUERY_1
MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLP
MFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC
>UniRef90_Q40250_2
MKVWPPIGLKKYETLSYLPPLSDEALSKEIDYLIRNKWIPCLEFEEHGFVYREHHHSPGYYDGRYWTMWKLP
MFGCTDSAQVMKEVGECKKEYPNAFIRVIGFDNIRQVQCISFIVAKPPGV
>UniRef90_A7YVW5_3
MQVWPPLGKRKFETLSYLPPLPVDALLKQIDYLIRSGWIPCIEFTVEGFVYREHHHSPGYYDGRYWTMWKLP
MYGCTDSTQVLAEVEANKKEYPNSYIRIIGFDNKRQVQCVSFIVHTPPS-
>UniRef90_P04714_4
MQVWPPYGKKKYETLSYLPDLTDEQLLKEIEYLLNKGWVPCLEFTEHGFVYREYHASPRYYDGRYWTMWKLP
MFGCTDATQVLGELQEAKKAYPNAWIRIIGFDNVRQVQCISFIAYKPPG-
>UniRef90_W9RUU9_5
MQVWPPRGKLKFETLSYLPDLTDEQLLKEIDYLLRSNWIPCLEFEVKAHIYRENNRSPGYYDGRYWTMWKLP
MFGCTDATQVLAEVQETKKAYPDAHVRIIGFDNNRQVQCISFIAYKPPA-
Submit multiple sequence alignment files in msf format:¶
python3 -m jpredapi submit --mode=msa --format=msf --file=tests/example_data/msa_msf.example --email=name@domain.com
Content of msa_msf.example file:
/tmp/filelPdICy MSF: 108 Type: N January 01, 1776 12:00 Check: 2741 ..
Name: 0_1a Len: 108 Check: 4063 Weight: 1.00
Name: 1_MA Len: 108 Check: 4875 Weight: 1.00
Name: 2_KE Len: 108 Check: 449 Weight: 1.00
Name: 3_NC Len: 108 Check: 3354 Weight: 1.00
//
0_1a APAFSVSPAS GASDGQSVSV SVAAAGETYY IAQCAPVGGQ DACNPATATS
1_MA APGVTVTPAT GLSNGQTVTV SATTPGTVYH VGQCAVVEGV IGCDATTSTD
2_KE SAAVSVSPAT GLADGATVTV SASATSTSAT ALQCAILAGR GACNVAEFHD
3_NC APTATVTPSS GLSDGTVVKV AGAQAGTAYD VGQCAWVDGV LACNPADFSS
0_1a FTTDASGAAS FSFTVRKSYA GQTPSGTPVG SVDCATDACN LGAGNSGLNL
1_MA VTADAAGKIT AQLKVHSSFQ AVVANGTPWG TVNCKVVSCS AGLGSDSGEG
2_KE FSLSG.GEGT TSVVVRRSFT GYVPDGPEVG AVDCDTAPCE IVVGGNTGEY
3_NC VTADANGSAS TSLTVRRSFE GFLFDGTRWG TVDCTTAACQ VGLSDAAGNG
0_1a GHVALTFG
1_MA AAQAITFA
2_KE GNAAISFG
3_NC PGVAISFN
Submit multiple sequence alignment files in blc format:¶
python3 -m jpredapi submit --mode=msa --format=blc --file=tests/example_data/msa_blc.example --email=name@domain.com
Content of msa_blc.example file:
>0_1a Name
>1_MA Name
>2_KE Name
>3_NC Name
* iteration 1
AASA
PPAP
AGAT
FVVA
STST
VVVV
STST
PPPP
AAAS
*
Check job status on JPred server¶
Check single job status using jobid:¶
python3 -m jpredapi status --jobid=jp_K46D05A
Check single job status using jobid and retrieve results:¶
python3 -m jpredapi status --jobid=jp_K46D05A --results=jpred_sspred/results
Check single job status using jobid, retrieve results, and decompress archive:¶
python3 -m jpredapi status --jobid=jp_K46D05A --results=jpred_sspred/results --extract
Retrieve results from JPred server¶
Retrieve results using jobid:¶
python3 -m jpredapi get_results --jobid=jp_K46D05A --results=jpred_sspred/results
Retrieve results using jobid and decompress archive:¶
python3 -m jpredapi get_results --jobid=jp_K46D05A --results=jpred_sspred/results --extract
Check how many jobs you have already submitted on a given day:¶
python3 -m jpredapi quota --email=name@domain.com
Using jpredapi as a library¶
Importing jpredapi module¶
If jpredapi package is installed on the system, it can be imported:
>>> import jpredapi
>>>
Submit jobs to JPred server¶
Submit single sequence in raw format using seq parameter:¶
>>> import jpredapi
>>>
>>> jpredapi.submit(mode="single", user_format="raw", seq="MQVWPIEGIKKFETLSYLPP")
>>>
Submit single sequence in raw format using file parameter:¶
>>> jpredapi.submit(mode="single", user_format="raw", file="tests/example_data/single_raw.example")
>>>
Submit single sequence in fasta format using file parameter:¶
>>> jpredapi.submit(mode="single", user_format="fasta", file="tests/example_data/single_fasta.example")
>>>
Submit multiple sequences in fasta format using file parameter:¶
>>> jpredapi.submit(mode="batch", user_format="fasta", file="tests/example_data/batch_fasta.example", email="name@domain.com")
>>>
Submit multiple sequence alignment files in fasta format:¶
>>> jpredapi.submit(mode="msa", user_format="fasta", file="tests/example_data/msa_fasta.example", email="name@domain.com")
>>>
Submit multiple sequence alignment files in msf format:¶
>>> jpredapi.submit(mode="msa", user_format="msf", file="tests/example_data/msa_msf.example", email="name@domain.com")
>>>
Submit multiple sequence alignment files in blc format:¶
>>> jpredapi.submit(mode="msa", user_format="blc", file="tests/example_data/msa_blc.example", email="name@domain.com")
>>>
Check job status on JPred server¶
Check single job status using jobid:¶
>>> import jpredapi
>>>
>>> jpredapi.status(jobid="jp_K46D05A")
>>>
Check single job status using jobid and retrieve results:¶
>>> jpredapi.status(jobid="jp_K46D05A", results_dir_path="jpred_sspred/results")
>>>
Check single job status using jobid, retrieve results, and decompress archive:¶
>>> jpredapi.status(jobid="jp_K46D05A", results_dir_path="jpred_sspred/results", extract=True)
>>>
Retrieve results from JPred server¶
Retrieve results using jobid:¶
>>> import jpredapi
>>>
>>> jpredapi.get_results(jobid="jp_K46D05A", results_dir_path="jpred_sspred/results")
>>>
Retrieve results using jobid and decompress archive:¶
>>> jpredapi.get_results(jobid="jp_K46D05A", results_dir_path="jpred_sspred/results", extract=True)
>>>
Check how many jobs you have already submitted on a given day:¶
>>> import jpredapi
>>>
>>> jpredapi.quota(email="name@domain.com")
>>>